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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ), 'gf_id' => 'HOM05D001211', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001211' ), 'data_identifier' => 'HOM05D001211', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001211', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '517', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p09430' => 'bna', 'A04p13770' => 'bna', 'A06p41320' => 'bna', 'A07p20530' => 'bna', 'A08p20030' => 'bna', 'A08p37190' => 'bna', 'A09p03340' => 'bna', 'A09p68170' => 'bna', 'A10p02390' => 'bna', 'Aa31LG1G9060' => 'aar', 'Aa31LG2G21910' => 'aar', 'Aa31LG2G5310' => 'aar', 'Aa31LG5G3100' => 'aar', 'Aa31LG9G880' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_344.5343' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.2658' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.3416' => 'aag', 'Actinidia05937' => 'ach', 'Actinidia10991' => 'ach', 'Actinidia11118' => 'ach', 'Actinidia16578' => 'ach', 'Actinidia18422' => 'ach', 'Actinidia30451' => 'ach', 'Actinidia33587' => 'ach', 'Actinidia36172' => 'ach', 'Actinidia39334' => 'ach', 'Ah.03g136500' => 'amhyb', 'AL1G13440' => 'aly', 'AL3G53550' => 'aly', 'AL5G16470' => 'aly', 'AL6G25000' => 'aly', 'AL7G24040' => 'aly', 'AL7G48950' => 'aly', 'AL8G15880' => 'aly', 'Aqoxy1G02299' => 'aox', 'Aqoxy3G01442' => 'aox', 'Aqoxy4G00593' => 'aox', 'Aqoxy5G03536' => 'aox', 'arahy.Tifrunner.gnm1.ann1.4C7JSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.C1DVSB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F5G46S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F9AFLL' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H3IS12' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.J0ZPKK' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K8NIBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MAIH3N' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PYDF2E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T30YXF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TFS39J' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WARQ2S' => 'arhy', 'AT1G03860' => 'ath', 'AT2G20530' => 'ath', 'AT3G27280' => 'ath', 'AT4G28510' => 'ath', 'AT5G14300' => 'ath', 'AT5G40770' => 'ath', 'AT5G44140' => 'ath', 'ATR0730G074' => 'atr', 'ATR1125G056' => 'atr', 'ATR1136G083' => 'atr', 'ATR1136G130' => 'atr', 'Atru.chr6.2491' => 'acertr', 'Atru.chr6.2860' => 'acertr', 'AUR62000240' => 'cqu', 'AUR62006587' => 'cqu', 'AUR62014883' => 'cqu', 'AUR62017458' => 'cqu', 'AUR62031092' => 'cqu', 'AUR62032526' => 'cqu', 'AUR62035949' => 'cqu', 'AUR62036071' => 'cqu', 'BcaB03g12576' => 'bca', 'BcaB04g19432' => 'bca', 'BcaB06g27554' => 'bca', 'BcaC04g23909' => 'bca', 'BcaC05g24495' => 'bca', 'BcaC06g31002' => 'bca', 'BcaC06g31003' => 'bca', 'BcaC06g33837' => 'bca', 'BcaC07g36938' => 'bca', 'BcaC07g38335' => 'bca', 'BcaC07g42224' => 'bca', 'BcaC08g44487' => 'bca', 'BcaC09g51653' => 'bca', 'BolC1t01060H' => 'bol', 'BolC4t26358H' => 'bol', 'BolC6t37133H' => 'bol', 'BolC7t44148H' => 'bol', 'BolC8t46879H' => 'bol', 'BolC8t52788H' => 'bol', 'BolC9t53276H' => 'bol', 'BraA01t00885Z' => 'bra', 'BraA04t17036Z' => 'bra', 'BraA06t27057Z' => 'bra', 'BraA07t29744Z' => 'bra', 'BraA08t35618Z' => 'bra', 'BraA09t35972Z' => 'bra', 'BraA09t42152Z' => 'bra', 'BraA10t42508Z' => 'bra', 'C01p10980' => 'bna', 'C04p47560' => 'bna', 'C05p02210' => 'bna', 'C06p19380' => 'bna', 'C07p36320' => 'bna', 'C08p00810' => 'bna', 'C08p10890' => 'bna', 'C08p52620' => 'bna', 'C09p03550' => 'bna', 'CAN.G151.8' => 'can', 'CAN.G1680.2' => 'can', 'CAN.G392.1' => 'can', 'CAN.G72.22' => 'can', 'CAN.G782.19' => 'can', 'CAN.G905.21' => 'can', 'CANSAT11G1804' => 'cansat', 'CANSAT64G0012' => 'cansat', 'CANSAT64G0457' => 'cansat', 'CARHR003190' => 'chi', 'CARHR111080' => 'chi', 'CARHR148550' => 'chi', 'CARHR179130' => 'chi', 'CARHR199030' => 'chi', 'CARHR213750' => 'chi', 'CARHR236290' => 'chi', 'Carub.0001s0300' => 'cru', 'Carub.0003s3499' => 'cru', 'Carub.0005s0554' => 'cru', 'Carub.0006s1249' => 'cru', 'Carub.0007s1217' => 'cru', 'Carub.0007s3472' => 'cru', 'Carub.0008s0438' => 'cru', 'Ca_01479_v3' => 'car', 'Ca_03603_v3' => 'car', 'Ca_14063_v3' => 'car', 'Ca_18851_v3' => 'car', 'Ca_18949_v3' => 'car', 'Ca_19876_v3' => 'car', 'Ca_24089_v3' => 'car', 'Ca_29765_v3' => 'car', 'Ca_30941_v3' => 'car', 'CBR_g12581' => 'cbr', 'CBR_g54102' => 'cbr', 'CBR_g72715' => 'cbr', 'Cc00_g14660' => 'ccan', 'Cc01_g01090' => 'ccan', 'Cc01_g01110' => 'ccan', 'Cc01_g03140' => 'ccan', 'Cc01_g05310' => 'ccan', 'Cc02_g13980' => 'ccan', 'Cc05_g07820' => 'ccan', 'Cc07_g00470' => 'ccan', 'Cc08_g07610' => 'ccan', 'Cc08_g11790' => 'ccan', 'Cc11_g06060' => 'ccan', 'CDE01G0785' => 'cde', 'CDE04G2773' => 'cde', 'CDE06G2675' => 'cde', 'CDE07G1003' => 'cde', 'Cfa007271' => 'cfa', 'Cfa016069' => 'cfa', 'Cfa020299' => 'cfa', 'Cfa025170' => 'cfa', 'Cfa026186' => 'cfa', 'Ciclev10015766m.g' => 'ccl', 'Ciclev10016485m.g' => 'ccl', 'Ciclev10028980m.g' => 'ccl', 'CiPaw.03G050900' => 'cil', 'CiPaw.04G033600' => 'cil', 'CiPaw.05G214300' => 'cil', 'CiPaw.06G035600' => 'cil', 'CiPaw.11G193200' => 'cil', 'ClCG06G017030' => 'cla', 'ClCG09G010990' => 'cla', 'COL.COLO4_04974' => 'col', 'COL.COLO4_07179' => 'col', 'COL.COLO4_07347' => 'col', 'COL.COLO4_15006' => 'col', 'COL.COLO4_24743' => 'col', 'COL.COLO4_25286' => 'col', 'COL.COLO4_29285' => 'col', 'COL.COLO4_35964' => 'col', 'Cpa.g.c41619' => 'cpa', 'Cpa.g.sc130.25' => 'cpa', 'Cre02.g088000' => 'cre', 'Cre12.g519350' => 'cre', 'CsaV3_1G001480' => 'csa', 'CsaV3_7G022010' => 'csa', 'CSS0003661' => 'camsi', 'CSS0010357' => 'camsi', 'CSS0011670' => 'camsi', 'CSS0028628' => 'camsi', 'CSS0037239' => 'camsi', 'CSS0037276' => 'camsi', 'CSS0037674' => 'camsi', 'CSS0039692' => 'camsi', 'CSS0040978' => 'camsi', 'CSS0044568' => 'camsi', 'DCAR_011295' => 'dca', 'DCAR_013046' => 'dca', 'DCAR_015079' => 'dca', 'Dinv06845' => 'din', 'Dinv20817' => 'din', 'Dinv25689' => 'din', 'Dinv33379' => 'din', 'Dinv39833' => 'din', 'Dinv40610' => 'din', 'Duzib093G1333' => 'dzi', 'Duzib140G0002' => 'dzi', 'Duzib187G1482' => 'dzi', 'Duzib235G1471' => 'dzi', 'Duzib248G0704' => 'dzi', 'Duzib264G1064' => 'dzi', 'ECA232G2598' => 'eca', 'ECA234G0901' => 'eca', 'ECA234G3699' => 'eca', 'ECA240G2113' => 'eca', 'ECA248G1073' => 'eca', 'EL10Ac4g10058' => 'bvu', 'EL10Ac6g13915' => 'bvu', 'EL10Ac7g17254' => 'bvu', 'EL10Ac8g20448' => 'bvu', 'Eucgr.A01869' => 'egr', 'Eucgr.J02293' => 'egr', 'Eucgr.K01066' => 'egr', 'FAN02G1328' => 'fan', 'FAN02G3666' => 'fan', 'FAN05G0845' => 'fan', 'FAN05G1249' => 'fan', 'FAN09G0472' => 'fan', 'FAN09G3251' => 'fan', 'FAN11G0191' => 'fan', 'FAN14G3442' => 'fan', 'FAN14G5950' => 'fan', 'FAN16G2701' => 'fan', 'FAN20G0740' => 'fan', 'FAN21G0537' => 'fan', 'FAN25G0900' => 'fan', 'FvH4_3g23290' => 'fve', 'FvH4_6g26770' => 'fve', 'FvH4_6g52780' => 'fve', 'Glyma.04G131800' => 'gma', 'Glyma.06G317500' => 'gma', 'Glyma.08G232000' => 'gma', 'Glyma.09G173500' => 'gma', 'Glyma.11G109400' => 'gma', 'Glyma.12G015900' => 'gma', 'Glyma.12G207500' => 'gma', 'Glyma.13G293600' => 'gma', 'Gohir.A03G154100' => 'ghi', 'Gohir.A05G352000' => 'ghi', 'Gohir.A09G033560' => 'ghi', 'Gohir.A10G160400' => 'ghi', 'Gohir.D02G177000' => 'ghi', 'Gohir.D04G060900' => 'ghi', 'Gohir.D09G034000' => 'ghi', 'Gohir.D10G085000' => 'ghi', 'Gorai.005G198700' => 'gra', 'Gorai.006G039000' => 'gra', 'Gorai.011G092900' => 'gra', 'Gorai.012G067800' => 'gra', 'GSVIVG01001841001' => 'vvi', 'GSVIVG01027465001' => 'vvi', 'GSVIVG01036736001' => 'vvi', 'HanXRQChr09g0255581' => 'han', 'HanXRQChr15g0475131' => 'han', 'HanXRQChr15g0487041' => 'han', 'HanXRQChr17g0549571' => 'han', 'HanXRQChr17g0554911' => 'han', 'HanXRQChr17g0557971' => 'han', 'Haze_00379' => 'cav', 'Haze_09721' => 'cav', 'Haze_14819' => 'cav', 'Haze_26899' => 'cav', 'Haze_27512' => 'cav', 'Hma1.2p1_0002F.1_g002350' => 'hma', 'Hma1.2p1_0279F.1_g112310' => 'hma', 'Hma1.2p1_1484F.1_g286310' => 'hma', 'Hma1.2p1_1658F.1_g296095' => 'hma', 'HPP92_004636' => 'vpl', 'HPP92_024826' => 'vpl', 'Hund07860' => 'sun', 'Hund12916' => 'sun', 'Hund21952' => 'sun', 'Lalb_Chr01g0007281' => 'lal', 'Lalb_Chr03g0024351' => 'lal', 'Lalb_Chr03g0032011' => 'lal', 'Lalb_Chr04g0264291' => 'lal', 'Lalb_Chr14g0367211' => 'lal', 'Lalb_Chr18g0048971' => 'lal', 'Lalb_Chr22g0356761' => 'lal', 'Lj1A1200T65' => 'lonja', 'Lj1A709T38' => 'lonja', 'Lj3g0017287' => 'lja', 'Lj3g0021576' => 'lja', 'Lj3g0024502' => 'lja', 'Lj3g0028008' => 'lja', 'Lj5g0026540' => 'lja', 'Lj7A606T84' => 'lonja', 'Lj8C107T2' => 'lonja', 'Lju41C48T14' => 'lonja', 'Lsat_1_v5_gn_0_11921' => 'lsa', 'Lsat_1_v5_gn_2_93661' => 'lsa', 'Lsat_1_v5_gn_4_185640' => 'lsa', 'Lsat_1_v5_gn_4_27181' => 'lsa', 'Lsat_1_v5_gn_8_136860' => 'lsa', 'Manes.12G086400' => 'mes', 'Manes.13G141300' => 'mes', 'Manes.17G107000' => 'mes', 'Mapoly0014s0186' => 'mpo', 'Mapoly0040s0040' => 'mpo', 'MBI01_g13081_MAGBIO' => 'mbi', 'MBI13_g01851_MAGBIO' => 'mbi', 'MCO10G016' => 'mco', 'MCO12G465' => 'mco', 'MD03G1195500' => 'mdo', 'MD05G1030500' => 'mdo', 'MD09G1016800' => 'mdo', 'MD11G1212000' => 'mdo', 'MD12G1189300' => 'mdo', 'MD17G1017200' => 'mdo', 'Medtr2g090760' => 'mtr', 'Medtr3g008250' => 'mtr', 'Medtr4g078200' => 'mtr', 'Medtr5g093030' => 'mtr', 'Medtr5g093040' => 'mtr', 'Medtr6g004320' => 'mtr', 'Medtr8g046300' => 'mtr', 'MELO3C013139.2' => 'cme', 'MELO3C017086.2' => 'cme', 'MELO3C023182.2' => 'cme', 'Migut.C00479' => 'egut', 'Migut.C00480' => 'egut', 'Migut.F01681' => 'egut', 'Migut.F01682' => 'egut', 'Migut.K01439' => 'egut', 'MSTRG.15124' => 'ama', 'MSTRG.15553' => 'ama', 'MSTRG.28143' => 'ama', 'MSTRG.3268' => 'ama', 'MSTRG.8121' => 'ama', 'Nitab4.5_0000051g0360' => 'nta', 'Nitab4.5_0000128g0290' => 'nta', 'Nitab4.5_0000494g0070' => 'nta', 'Nitab4.5_0000621g0010' => 'nta', 'Nitab4.5_0000743g0060' => 'nta', 'Nitab4.5_0001184g0020' => 'nta', 'Nitab4.5_0002350g0050' => 'nta', 'Nitab4.5_0002773g0090' => 'nta', 'Nitab4.5_0005651g0030' => 'nta', 'Nitab4.5_0008732g0010' => 'nta', 'Nitab4.5_0010702g0040' => 'nta', 'Nitab4.5_0012484g0020' => 'nta', 'Nn3g20266' => 'nnu', 'Nn8g40513' => 'nnu', 'Nn8g40896' => 'nnu', 'Oeu016003.1' => 'oeu', 'Oeu016900.1' => 'oeu', 'Oeu019173.1' => 'oeu', 'Oeu048584.1' => 'oeu', 'Oeu064850.1' => 'oeu', 'Os02g0580500' => 'osa', 'Os03g0813200' => 'osa', 'Os03g0814600' => 'osa', 'Os03g0841700' => 'osa', 'Os04g0462900' => 'osa', 'Os07g0262200' => 'osa', 'Peaxi162Scf00044g01217' => 'pax', 'Peaxi162Scf00189g00020' => 'pax', 'Peaxi162Scf00241g00149' => 'pax', 'Peaxi162Scf00383g00092' => 'pax', 'Peaxi162Scf00594g10011' => 'pax', 'Peaxi162Scf01066g00011' => 'pax', 'PGR042G0275' => 'pgr', 'PGR083G0086' => 'pgr', 'PGR142G3280' => 'pgr', 'PGSC0003DMG400013746' => 'stu', 'PGSC0003DMG400016222' => 'stu', 'PGSC0003DMG400016803' => 'stu', 'PGSC0003DMG400021855' => 'stu', 'PGSC0003DMG400029027' => 'stu', 'Phvul.005G009100' => 'pvu', 'Phvul.005G099600' => 'pvu', 'Phvul.011G018300' => 'pvu', 'Potri.001G335700' => 'ptr', 'Potri.007G134700' => 'ptr', 'Potri.017G017400' => 'ptr', 'Potri.017G065800' => 'ptr', 'Pp3c16_1240' => 'ppa', 'Pp3c23_22260' => 'ppa', 'Pp3c23_5760' => 'ppa', 'Pp3c25_1160' => 'ppa', 'Pp3c5_6150' => 'ppa', 'Pp3c6_17690' => 'ppa', 'Pp3c8_25300' => 'ppa', 'Pp3c9_8950' => 'ppa', 'PRCOL_00002068' => 'pco', 'PRCOL_00003179' => 'pco', 'Prupe.3G128200' => 'ppe', 'Prupe.3G300700' => 'ppe', 'Prupe.4G220500' => 'ppe', 'Psat4g180080' => 'psa', 'Psat4g180120' => 'psa', 'Psat5g228720' => 'psa', 'Psat5g274320' => 'psa', 'Psat6g214120' => 'psa', 'Psat7g169840' => 'psa', 'PSO063G6477' => 'pso', 'PSO210G6525' => 'pso', 'PSO339G0288' => 'pso', 'PSO541G6153' => 'pso', 'PSO782G5282' => 'pso', 'PSO801G0810' => 'pso', 'PSO832G1887' => 'pso', 'QL02p072780' => 'qlo', 'QL05p043135' => 'qlo', 'QL08p006857' => 'qlo', 'QL08p007880' => 'qlo', 'QL09p021129' => 'qlo', 'RcHm_v2.0_Chr0c19g0500161' => 'rch', 'RcHm_v2.0_Chr2g0128531' => 'rch', 'RcHm_v2.0_Chr2g0174411' => 'rch', 'RcHm_v2.0_Chr5g0041011' => 'rch', 'Rhsim04G0071500' => 'rsi', 'Rhsim06G0136000' => 'rsi', 'Rhsim08G0045900' => 'rsi', 'Rhsim10G0010500' => 'rsi', 'Rhsim11G0131200' => 'rsi', 'Sabra16G0216700' => 'sbr', 'Sabra17G0013600' => 'sbr', 'Sabra17G0061600' => 'sbr', 'SalBow6G1886' => 'sbo', 'SalBow6G2352' => 'sbo', 'SalBow7G1656' => 'sbo', 'Sc03g0006860' => 'sci', 'Sc03g0007070' => 'sci', 'Sc12g0003280' => 'sci', 'Sc12g0003290' => 'sci', 'Sed0002938' => 'sed', 'Sed0015388' => 'sed', 'Sed0018942' => 'sed', 'Sed0025786' => 'sed', 'SEGI_25944' => 'sgi', 'SEGI_28160' => 'sgi', 'SGA_v2.0_scaffold154G37159' => 'sas', 'SGA_v2.0_scaffold47G17554' => 'sas', 'SGA_v2.0_scaffold58G20552' => 'sas', 'SGA_v2.0_scaffold70G23479' => 'sas', 'SGA_v2.0_scaffold74G24615' => 'sas', 'SMO164G0014' => 'smo', 'SMO367G1022' => 'smo', 'Solyc05g051510.4' => 'sly', 'Solyc10g008140.3' => 'sly', 'Solyc11g010190.1' => 'sly', 'Solyc11g013260.3' => 'sly', 'Solyc12g005500.3' => 'sly', 'Sopen05g029930' => 'spe', 'Sopen10g004010' => 'spe', 'Sopen11g004970' => 'spe', 'Sopen11g008280' => 'spe', 'Sp1g02720' => 'spa', 'Sp2g16430' => 'spa', 'Sp3g33760' => 'spa', 'Sp7g01130' => 'spa', 'Sp7g26490' => 'spa', 'TAR371G1200' => 'tar', 'TAR374G0722' => 'tar', 'TAR624G1303' => 'tar', 'TAR626G0376' => 'tar', 'TAR627G0924' => 'tar', 'TAR629G2584' => 'tar', 'THA.LOC104814515' => 'tha', 'THA.LOC104815963' => 'tha', 'THA.LOC104823968' => 'tha', 'THA.LOC104824684' => 'tha', 'THA.LOC104825303' => 'tha', 'THA.LOC104826042' => 'tha', 'Thecc.02G187800' => 'tca', 'Thecc.04G028200' => 'tca', 'Thhalv10002059m.g' => 'esa', 'Thhalv10004748m.g' => 'esa', 'Thhalv10008384m.g' => 'esa', 'Thhalv10008592m.g' => 'esa', 'Thhalv10015345m.g' => 'esa', 'Thhalv10025900m.g' => 'esa', 'Thhalv10027882m.g' => 'esa', 'TPR.G12247' => 'tpr', 'TPR.G28020' => 'tpr', 'TPR.G3050' => 'tpr', 'TPR.G6484' => 'tpr', 'TWI12G0624' => 'twi', 'TWI14G1263' => 'twi', 'TWI15G0594' => 'twi', 'TWI15G0838' => 'twi', 'TWI23G1090' => 'twi', 'TWI36G0239' => 'twi', 'TWI60G0665' => 'twi', 'unitig_32.g10668' => 'ugi', 'unitig_746.g26797' => 'ugi', 'unitig_88.g27780' => 'ugi', 'unitig_899.g15172' => 'ugi', 'vmacro05927' => 'vma', 'vmacro09242' => 'vma', 'vmacro12352' => 'vma', 'VMungo0540G1051' => 'vmu', 'VMungo0720G1486' => 'vmu', 'VMungo1080G0475' => 'vmu', 'VMungo1080G0620' => 'vmu', 'VMungo1080G0820' => 'vmu', 'VMungo1080G1326' => 'vmu', 'VMungo1080G1420' => 'vmu', 'VMungo1080G1593' => 'vmu', 'VMungo1127G0606' => 'vmu', 'VMungo1215G2071' => 'vmu', 'Zm00001eb064000' => 'zma', 'Zm00001eb097180' => 'zma', 'Zm00001eb245230' => 'zma', 'Zm00001eb424310' => 'zma' ) $gf_id = 'HOM05D001211' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001211' ) $data_identifier = 'HOM05D001211' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 5, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 1, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 7, 'atr' => (int) 4, 'acertr' => (int) 2, 'cqu' => (int) 8, 'bca' => (int) 13, 'bol' => (int) 7, 'bra' => (int) 8, 'can' => (int) 6, 'cansat' => (int) 3, 'chi' => (int) 7, 'cru' => (int) 7, 'car' => (int) 9, 'cbr' => (int) 3, 'ccan' => (int) 11, 'cde' => (int) 4, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 8, 'cpa' => (int) 2, 'cre' => (int) 2, 'csa' => (int) 2, 'camsi' => (int) 10, 'dca' => (int) 3, 'din' => (int) 6, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 13, 'fve' => (int) 3, 'gma' => (int) 8, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 6, 'cav' => (int) 5, 'hma' => (int) 4, 'vpl' => (int) 2, 'sun' => (int) 3, 'lal' => (int) 7, 'lonja' => (int) 5, 'lja' => (int) 5, 'lsa' => (int) 5, 'mes' => (int) 3, 'mpo' => (int) 2, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 7, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 5, 'nta' => (int) 12, 'nnu' => (int) 3, 'oeu' => (int) 5, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 4, 'ppa' => (int) 8, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 7, 'qlo' => (int) 5, 'rch' => (int) 4, 'rsi' => (int) 5, 'sbr' => (int) 3, 'sbo' => (int) 3, 'sci' => (int) 4, 'sed' => (int) 4, 'sgi' => (int) 2, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 5, 'tar' => (int) 6, 'tha' => (int) 6, 'tca' => (int) 2, 'esa' => (int) 7, 'tpr' => (int) 4, 'twi' => (int) 7, 'ugi' => (int) 4, 'vma' => (int) 3, 'vmu' => (int) 10, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb424310' $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